In order to use SBpipe, the following packages must be installed:

Please, make sure that Python pip and Rscript work fine. SBpipe can work with the simulators:

  • COPASI 4.19+ - (for model simulation, parameter scan, and parameter estimation)
  • Python (directly or as a wrapper to call models coded in any programming language)

If LaTeX/PDF reports are also desired, the following package must also be installed:

  • LaTeX 2013+

Installation on GNU/Linux

Installation of COPASI

As of 2016, COPASI is not available as a package in GNU/Linux distributions. Users must add the path to COPASI binary files manually editing the GNU/Linux $HOME/.bashrc file as follows:

# Path to CopasiSE (update this accordingly)
export PATH=$PATH:/path/to/CopasiSE/

The correct installation of CopasiSE can be tested with:

# Reload the .bashrc file
source $HOME/.bashrc

CopasiSE -h
> COPASI 4.19 (Build 140)

Installation of LaTeX

Users are recommended to install LaTeX/texlive using the package manager of their GNU/Linux distribution. On GNU/Linux Ubuntu machines the following package is required:


The correct installation of LaTeX can be tested with:

pdflatex -v
> pdfTeX 3.14159265-2.6-1.40.16 (TeX Live 2015/Debian)
> kpathsea version 6.2.1
> Copyright 2015 Peter Breitenlohner (eTeX)/Han The Thanh (pdfTeX).

Installation of SBpipe via Python pip

SBpipe and its Python dependencies can simply be installed via Python pip using the command:

# install sbpipe from via pip
pip install sbpipe

In order to analyse the data, SBpipe requires the R package sbpiper, which can be installed as follows:

# install sbpiper from r-cran
Rscript -e "install.packages('sbpiper', dep=TRUE, repos='')"

Installation of SBpipe via Conda

Users need to download and install Miniconda3 ( SBpipe will be installed in a dedicated conda environment:

# create a new environment `sbpipe`
conda create -n sbpipe

# activate the environment.
# For old versions of conda, replace `conda` with `source`.
conda activate sbpipe

# install sbpipe and its dependencies (including sbpiper)
conda install -c bioconda sbpipe

Installation of SBpipe from source

Users need to install git.

# clone SBpipe from GitHub
git clone
# move to sbpipe folder
cd sbpipe
# install SBpipe dependencies on GNU/Linux, run:

Finally, to run sbpipe from any shell, users need to add ‘sbpipe/scripts’ to the PATH environment variable by adding the following lines to the $HOME/.bashrc file:

# SBPIPE (update this accordingly)
export PATH=$PATH:/path/to/sbpipe/scripts

The .bashrc file should be reloaded to apply the previous edits:

# Reload the .bashrc file
source $HOME/.bashrc

Installation on Windows

See installation on GNU/Linux and install SBpipe via PIP or Conda. Windows users need to install LaTeX MikTeX

Testing SBpipe

The correct installation of SBpipe and its dependencies can be verified by running the following commands. For the correct execution of all tests, LaTeX must be installed.

# SBpipe version:
sbpipe -V
> sbpipe 4.13.0

Unless SBpipe was installed from source, users need to download the source code at the page to run the test suites.

# unzip and change path
cd sbpipe-X.Y.Z/tests
# run model simulation using COPASI (see results in tests/copasi_models):
nosetests --nocapture
# run all tests:
nosetests --nocapture
# generate the manuscript figures (see results in tests/insulin_receptor):
nosetests --nocapture